I doubt he will be the Gym Leader
He will. The official profile on the anime's cast page refers to him as such.
That kinda seriously annoys me just because of how the character is now, he is using a Bunnelby...
Yes, Ash has traveled with Gym Leaders before, but it was usually after the battle or close to it. Ash won't be battling Clemont until half the season is over.
I know this is getting in the realm of fantasy wrestling, but I think it would have been interesting if Ash challenged Clemont to a battle right off and lost, then Clemont asks to join him on his journey to watch Ash grow. So during the series Clemont is always the stronger trainer, but Ash continues to get stronger. Then as the two connect as friends they have the epic rematch.
I just have a feeling when they reveal Clemont to be the Gym Leader of Lumiose City it will really be anti-climactic. Part of me still thinks you will see Trevor be the Gym Leader over Clemont for several reasons. The first is Trevor also lives in Lumiose City, Trevor has a Pikachu in the game, and Trevor is about Clemont's age.
That's because it's a recently caught one. It's not his main Pokemon for the gym. In the previews of upcoming episodes it showed him training his Bunnelby with Heliolisk, one of his main Gym Pokemon.